The Solanaceae Genomics Resource at MSU is a portal to several projects in the Buell Lab on the genomics of the Solanaceae.
Potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2004, worldwide potato production exceeded 327 million metric tons. Potato also produces more food energy and food value per unit of land area than any other crop. Compared to grain crops, potato is a superior source of nutrition; however, among major crop plants, potato is arguably the most intensively managed. In addition, tuber quality requirements are complex and must be maintained during harvest and storage.
To improve our understanding of potato, we participated in the International Potato Genome Sequencing Consortium (PGSC). The PGSC engaged in sequencing two potato species: the heterozygous diploid S. tuberosum Group Tuberosum RH89-039-16 (RH), and the doubled monoploid Solanum tuberosum Group Phureja DM1-3 (DM). For more information please see the genome release paper in Nature. The DM genome was assembled, annotated and released and can be accessed through this site. The current potato genome assembly represents 726 Mb of which 86% is anchored to the genetic map. A total of 39,031 genes were annotated in the DM genome. To aid in the annotation of the potato genome, a comprehensive whole transcriptome sequencing project was undertaken in which 32 RNA-seq libraries from the DM clone were sequenced. The RH genome has also been sequenced and reads have been mapped to the DM genome assembly. Reads for the RH genome are available through the NCBI SRA (SRP019978) and transcript data is available through the EBI.
The Solanaceae Genomics Resource, funded by USDA-NIFA, provides a robust, rich, and integrated resource allowing broad and deep data-mining of Solanaceae sequences. The resource facilitates community access to the results of added-value comparative and de novo analyses on the genomic sequences provided by the tomato and potato genome sequencing efforts and Solanaceae transcript assemblies from PlantGDB, and links Solanaceae sequences to the functional genomics resources of other related model dicot species.
The SolCAP project linked together people from public and private institutions along with industry members who are dedicated to the improvement of the Solanaceae crops: potato and tomato. Through innovative research, education and training the SolCAP project focused on translating genomic advances to US tomato and potato breeding programs. This will lead to significantly improved varieties that benefit processors, consumer and the environment.
We welcome input from outside researchers. If there is some way in which we can improve this resource, we would like to hear from you. Please use the comment form on our contact page to send us your suggestions.
This material is based upon work supported by the National Science Foundation under Grant Nos. DBI-0604907 and DBI-0834044 and the National Research Initiative Plant Genome Program of the USDA National Institute of Food and Agriculture Grant 2008-35300-18671. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF) or the U. S. Department of Agriculture.
We have added several additional tracks to the SGR genome browsers. We have added a tomato repeat track to the Solanum lycopersicum genome browser along with tracks diplaying Nicotiana benthamiana gene models and transcriptome shotgun assemblies to the potato and tomato genome browswers. Previously, numerous additional analyses and tools were added to the website. We incorporated BAC end sequences from three tomato libraries, included over 4 million SNPs for tomato based on S. pimpinellifolium WGS reads and over 8,000 SNPs used by the SolCAP groups to design an Infinium array, incorporated transcriptome data from 10 tissues of tomato, and a new SNP search tool was implemented for potato and tomato SNPs to help users to access SNPs within regions or genes easier. For more detailed information please see the What's New
We have planned server maintenance on the first Wednesday of every month and therefore, SGR web pages may be unavailable or only partially functional during server maintenance. There will be additional maintenance on the following dates where the SGR web pages will be unavailable: August 5, 2013, December 2, 2013, April 7, 2014.